Gene structure, evolution and expression analysis of the P-ATPase gene family in Chinese pear (Pyrus bretschneideri)

The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

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Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.)

Genomics ◽

10.1016/j.ygeno.2020.02.008 ◽

2020 ◽

Vol 112 (3) ◽

pp. 2550-2563 ◽

Cited By ~ 1

Author(s):

Yuxin Zhang ◽

Qionghou Li ◽

Linlin Xu ◽

Xin Qiao ◽

Chunxin Liu ◽

...

Keyword(s):

Comparative Analysis ◽

Gene Family ◽

Expression Analysis ◽

Rosaceae Species ◽

Atpase Gene ◽

P Type

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Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

10.21203/rs.3.rs-49275/v1 ◽

2020 ◽

Author(s):

Xiaowei Jia ◽

Xuyang Si ◽

Yangyang Jia ◽

Hongyan Zhang ◽

Shijun Tian ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Gene Structure ◽

Hexaploid Wheat ◽

Catalytic Domain ◽

Diacylglycerol Kinase ◽

Regulatory Elements ◽

Amino Acid Sequences ◽

Developmental Expression ◽

Chinese Spring Wheat

Abstract Background The inositol phospholipid signaling system, which is based on the metabolism of phosphoinositide (PI), mediates plant growth, development, and responses to adversity. Diacylglycerol kinase (DGK) is one of the key enzymes in the PI-cycle, which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGK genes have not been reported in wheat. Results In this study, 20 DGK gene family members from the heterologous hexaploid wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and a accessory domain. The analyses of phylogenetic and gene structure revealed that each TaDGK gene could be grouped to clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation in functional domains, for example gene structure and amino acid sequences. By cloning, four coding sequences were ascertained from Chinese spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification in wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated express under salt and drought stresses, suggesting their possible roles in dealing with adversity environment. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. Conclusions These results provide valuable information for understanding the putative functions of DGK genes in wheat, and conduce to ulterior functional analysis of this pivotal gene family. The 20 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

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Gene structure and expression analysis of the drought- and abscisic acid-responsive CDeT11-24 gene family from the resurrection plant Craterostigma plantagineum Hochst

Planta ◽

10.1007/s004250050280 ◽

1998 ◽

Vol 204 (4) ◽

pp. 459-471 ◽

Cited By ~ 26

Author(s):

Riccardo Velasco ◽

Francesco Salamini ◽

Dorothea Bartels

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Expression Analysis ◽

Gene Structure ◽

Resurrection Plant ◽

Craterostigma Plantagineum ◽

Gene Structure And Expression

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Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)

Plants ◽

10.3390/plants9121661 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1661

Author(s):

Hongsheng Zhou ◽

Wen Huang ◽

Shufen Luo ◽

Huali Hu ◽

Yingtong Zhang ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Prunus Persica ◽

Proton Pumps ◽

Event Analysis ◽

Specific Expression ◽

Rosaceae Species ◽

Genome Wide ◽

A Genome ◽

Atpase Gene

Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence.

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Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽

10.1186/s12864-021-07653-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cuili Pan ◽

Zhaoxiong Lei ◽

Shuzhe Wang ◽

Xingping Wang ◽

Dawei Wei ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Adipocyte Differentiation ◽

Bos Taurus ◽

Adipogenic Differentiation ◽

Critical Role ◽

Bos Indicus ◽

Specific Expression ◽

Genome Wide ◽

A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

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